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- PDB-6rc9: P1 Mycoplasma pneumoniae -

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Basic information

Entry
Database: PDB / ID: 6rc9
TitleP1 Mycoplasma pneumoniae
ComponentsAdhesin P1
KeywordsCELL ADHESION / adhesin / extracellular / transmembrane-complex / immunodominant protein.
Function / homology
Function and homology information


attachment organelle / adhesion of symbiont to microvasculature / cell projection / cell surface / membrane / plasma membrane
Similarity search - Function
Adhesin P1, C-terminal domain / Adhesin P1, N-terminal / Adhesin P1 / Mycoplasma adhesin P1, C-terminal / Mycoplasma adhesin P1, N-terminal
Similarity search - Domain/homology
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsVizarraga, D. / Aparicio, D. / Illanes, R. / Fita, I.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessMDM-2014-0435 Spain
CitationJournal: Nat Commun / Year: 2020
Title: Immunodominant proteins P1 and P40/P90 from human pathogen Mycoplasma pneumoniae.
Authors: David Vizarraga / Akihiro Kawamoto / U Matsumoto / Ramiro Illanes / Rosa Pérez-Luque / Jesús Martín / Rocco Mazzolini / Paula Bierge / Oscar Q Pich / Mateu Espasa / Isabel Sanfeliu / ...Authors: David Vizarraga / Akihiro Kawamoto / U Matsumoto / Ramiro Illanes / Rosa Pérez-Luque / Jesús Martín / Rocco Mazzolini / Paula Bierge / Oscar Q Pich / Mateu Espasa / Isabel Sanfeliu / Juliana Esperalba / Miguel Fernández-Huerta / Margot P Scheffer / Jaume Pinyol / Achilleas S Frangakis / Maria Lluch-Senar / Shigetarou Mori / Keigo Shibayama / Tsuyoshi Kenri / Takayuki Kato / Keiichi Namba / Ignacio Fita / Makoto Miyata / David Aparicio /
Abstract: Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which ...Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which form a transmembrane adhesion complex. Here we report the structure of P1, determined by X-ray crystallography and cryo-electron microscopy, and the X-ray structure of P40/P90. Contrary to what had been suggested, the binding site for sialic acid was found in P40/P90 and not in P1. Genetic and clinical variability concentrates on the N-terminal domain surfaces of P1 and P40/P90. Polyclonal antibodies generated against the mostly conserved C-terminal domain of P1 inhibited adhesion of M. pneumoniae, and serology assays with sera from infected patients were positive when tested against this C-terminal domain. P40/P90 also showed strong reactivity against human infected sera. The architectural elements determined for P1 and P40/P90 open new possibilities in vaccine development against M. pneumoniae infections.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)159,7941
Polymers159,7941
Non-polymers00
Water7,314406
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area49080 Å2
Unit cell
Length a, b, c (Å)132.897, 115.637, 96.341
Angle α, β, γ (deg.)90.00, 117.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Adhesin P1 / Attachment protein / Cytadhesin P1


Mass: 159794.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Gene: mgpA, MPN_141, MP013 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11311
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEGMME2000 and PCB buffer

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97897 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 1.935→72.2 Å / Num. obs: 92405 / % possible obs: 96.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 32.96 Å2 / CC1/2: 0.993 / Net I/σ(I): 6.9
Reflection shellResolution: 1.94→2.04 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHASERphasing
DMMultiphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→72.2 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4593 4.97 %RANDOM
Rwork0.187 ---
obs0.189 92369 96.3 %-
Displacement parametersBiso mean: 60.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.9133 Å20 Å2-7.0277 Å2
2---11.1761 Å20 Å2
3---9.2628 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.94→72.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10450 0 0 406 10856
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110801HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1514735HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3581SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1857HARMONIC5
X-RAY DIFFRACTIONt_it10801HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion20.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1382SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12597SEMIHARMONIC4
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2569 345 5.14 %
Rwork0.2318 6370 -
all0.2331 6715 -
obs--95.05 %
Refinement TLS params.Method: refined / Origin x: 24.895 Å / Origin y: 38.8375 Å / Origin z: 22.8525 Å
111213212223313233
T-0.258 Å2-0.0146 Å2-0.0116 Å2--0.192 Å20.0383 Å2---0.2924 Å2
L1.5366 °2-0.1419 °2-1.2345 °2-0.2174 °20.0262 °2--2.7572 °2
S-0.0596 Å °-0.2333 Å °-0.0895 Å °-0.0029 Å °-0.0527 Å °-0.0509 Å °0.0002 Å °0.5379 Å °0.1123 Å °
Refinement TLS groupSelection details: { A|* }

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